A tool for miRNA prediction that requires only sRNA datasets as input. Mature miRNAs are predicted from such datasets through a multi-stage process, involving filtering, miRNA:miRNA* duplex generation and duplex classification using a support vector machine. Tests on sRNA datasets from model animals demonstrate that the tool is effective at predicting genuine miRNA duplexes, and, for some sets, achieves a high degree of precision when considering only the mature sequence.

MirPlex in pipeline

[…] yield a dataset of 848,129 sequences and removed those present in less than 5 copies. we also removed sequences that could be assembled together to form longer contigs, mimicking what is done by the mirplex pipeline []. the remaining 94,239 sequences contained 53 different small rnas that were able to form duplexes with the 2 base 3’ overhangs expected for mirnas, and most of these were 22 […]

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MirPlex in publications

[…] bases and contained only reads in the same direction. these 948 assemblies indicated the small rnas contributing to them did not have the defined ends expected for bone fide mirnas, so as with the mirplex pipeline [], they were also removed leaving a final dataset of 94,239 potential mirna candidates. to test if any of the 94,239 sequences could form rna duplexes with 2 base 3’ overhangs, […]

[…] overall, the most abundant and conserved mirnas were identified in this study, but the approach might be less successful for species that do not have closely related species with genome sequences., mirplex is a tool that requires only srna datasets as input with no genome sequences needed (mapleson et al., ). it uses a multi-stage process to identify genuine mirna duplexes. first, […]

[…] based on the analysis of a hold-out test set. using experimental data, we also show that our approach can detect about an order of magnitude or more known mirnas than the mature mirna predictor, mirplex., non-coding rnas (ncrnas) are functional rna transcripts that do not translate into proteins. the small ncrna class consists of ncrnas of lengths of about 20 to 30 nucleotides (nt). two […]

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